I'm new to both PayPal IPN and Magento, so I may be making an obvious mistake, but I've also been having a ton of problems with the Magento install that were caused by problems with the auto-installer package HostGator provided.

@benmarks Sorry, no definitive answers. If I recall correctly, we narrowed it down to an issue where the IPN notification was being sent, but failing to receive the appropriate 200 response from the server. PayPal support made a convincing case for it being an issue with the server configuration, but the hosting company (HostGator) refused to acknowledge any responsibility, and would provide no additional support. Before I left the company, we had abandoned PayPal in pursuit of a payment processor offered by our bank, but were waiting on a PCI compliance eval before we could implement.
– BeofettSep 4 '15 at 0:37